venn.cpp

   1 /*
   2  *  venn.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venn.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 #include "sharedchao1.h"
  15 #include "sharedsobscollectsummary.h"
  16
  17
  18 //**********************************************************************************************************************
  19 Venn::Venn(string o) : outputDir(o) {
  20         try {
  21                 globaldata = GlobalData::getInstance();
  22                 m = MothurOut::getInstance();
  23
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "Venn", "Venn");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
  32         try {
  33
  34                 vector<string> outputNames;
  35
  36                 for(int i=0;i<vCalcs.size();i++){
  37                         string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
  38                         outputNames.push_back(filenamesvg);
  39                         openOutputFile(filenamesvg, outsvg);
  40
  41                         if (m->control_pressed) { outsvg.close(); return outputNames; }
  42
  43                         vector<double> data = vCalcs[i]->getValues(sabund);
  44
  45                         int width = 1500;
  46                         int height = 1500;
  47
  48                         //svg image
  49                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
  50                         outsvg << "<g>\n";
  51
  52                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
  53                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
  54                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" +  toString(int(0.50 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
  55                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" + toString((width / 2) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(data[0]) + "</text>\n";
  56
  57                         if (data.size() == 3) {
  58                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.60 * height)) +  "\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
  59                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.645 * height)) +  "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
  60                         }
  61
  62                         outsvg << "</g>\n</svg>\n";
  63                         outsvg.close();
  64                 }
  65
  66                 return outputNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "Venn", "getPic");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
  75         try {
  76
  77                 vector<SharedRAbundVector*> subset;
  78                 vector<string> outputNames;
  79
  80                 int width = 1500;
  81                 int height = 1500;
  82
  83                 /******************* 1 Group **************************/
  84                 if (lookup.size() == 1) {
  85
  86                         SAbundVector s;
  87                         s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
  88
  89                         //make a file for each calculator
  90                         for(int i=0;i<vCalcs.size();i++){
  91                                 string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
  92                                 outputNames.push_back(filenamesvg);
  93                                 openOutputFile(filenamesvg, outsvg);
  94
  95                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
  96
  97                                 //in essence you want to run it like a single
  98                                 if (vCalcs[i]->getName() == "sharedsobs") {
  99                                         singleCalc = new Sobs();
 100                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 101                                         singleCalc = new Chao1();
 102                                 }else if (vCalcs[i]->getName() == "sharedace") {
 103                                         singleCalc = new Ace(10);
 104                                 }
 105
 106                                 vector<double> data = singleCalc->getValues(sabund);
 107
 108                                 //svg image
 109                                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \">\n";
 110                                 outsvg << "<g>\n";
 111
 112                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 113                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 114                                 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" +  toString(int(0.50 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 115                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.50 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.24 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 116                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.50 * width) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(data[0]) + "</text>\n";
 117
 118                                 if (data.size() == 3) {
 119                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.60 * height)) +  "\" >The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 120                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.645 * height)) +  "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 121                                 }
 122
 123                                 outsvg << "</g>\n</svg>\n";
 124                                 outsvg.close();
 125                                 delete singleCalc;
 126
 127                         }
 128                 /******************* 2 Groups **************************/
 129
 130                 }else if (lookup.size() == 2) {
 131                         //get sabund vector pointers so you can use the single calculators
 132                         //one for each group
 133                         SAbundVector sA, sB;
 134                         SAbundVector* sabundA; SAbundVector* sabundB;
 135                         sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
 136                         sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
 137
 138                         subset.clear();
 139                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 140
 141                         //make a file for each calculator
 142                         for(int i=0;i<vCalcs.size();i++){
 143                                 string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 144                                 outputNames.push_back(filenamesvg);
 145                                 openOutputFile(filenamesvg, outsvg);
 146
 147                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
 148
 149                                 //get estimates for sharedAB
 150                                 vector<double> shared = vCalcs[i]->getValues(subset);
 151
 152                                 //in essence you want to run it like a single
 153                                 if (vCalcs[i]->getName() == "sharedsobs") {
 154                                         singleCalc = new Sobs();
 155                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 156                                         singleCalc = new Chao1();
 157                                 }//else if (vCalcs[i]->getName() == "sharedace") {
 158                                         //singleCalc = new Ace(10);
 159                                 //}
 160
 161                                 //get estimates for numA
 162                                 vector<double> numA = singleCalc->getValues(sabundA);
 163
 164                                 //get estimates for numB
 165                                 vector<double> numB = singleCalc->getValues(sabundB);
 166
 167                                 //image window
 168                                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
 169                                 outsvg << "<g>\n";
 170
 171                                 //draw circles
 172                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 173                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 174                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.36 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 175                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.62 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 176                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(numA[0] - shared[0]) + "</text>\n";
 177                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(numB[0] - shared[0]) + "</text>\n";
 178                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.25 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 179                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.25 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 180                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(shared[0]) + "</text>\n";
 181                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.66 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 182                                 if (numA.size() == 3) {
 183                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 184                                 }else { outsvg << "</text>\n"; }
 185
 186                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.69 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 187                                 if (numB.size() == 3) {
 188                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 189                                 }else { outsvg << "</text>\n"; }
 190
 191                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.72 * height)) +  "\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
 192                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
 193                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.78 * height)) +  "\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "</text>\n";
 194
 195                                 //close file
 196                                 outsvg << "</g>\n</svg>\n";
 197                                 outsvg.close();
 198                                 delete singleCalc;
 199                         }
 200                 /******************* 3 Groups **************************/
 201
 202                 }else if (lookup.size() == 3) {
 203
 204                         height = 1600;
 205
 206                         //get sabund vector pointers so you can use the single calculators
 207                         //one for each group
 208                         SAbundVector sA, sB, sC;
 209                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 210                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 211                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 212                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 213
 214                         //make a file for each calculator
 215                         for(int i=0;i<vCalcs.size();i++){
 216
 217                                 string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 218                                 outputNames.push_back(filenamesvg);
 219                                 openOutputFile(filenamesvg, outsvg);
 220
 221                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
 222
 223                                 if (vCalcs[i]->getName() == "sharedace") {
 224
 225                                         singleCalc = new Ace(10);
 226
 227                                         //get estimates for numA
 228                                         vector<double> numA = singleCalc->getValues(sabundA);
 229
 230                                         //get estimates for numB
 231                                         vector<double> numB = singleCalc->getValues(sabundB);
 232
 233                                         //get estimates for numC
 234                                         vector<double> numC = singleCalc->getValues(sabundC);
 235
 236
 237                                         //get estimates for sharedAB, sharedAC and sharedBC
 238                                         subset.clear();
 239                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 240                                         vector<double> sharedAB = vCalcs[i]->getValues(subset);
 241
 242                                         subset.clear();
 243                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 244                                         vector<double> sharedAC = vCalcs[i]->getValues(subset);
 245
 246                                         subset.clear();
 247                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 248                                         vector<double> sharedBC = vCalcs[i]->getValues(subset);
 249
 250                                         vector<double> sharedAwithBC;
 251                                         vector<double> sharedBwithAC;
 252                                         vector<double> sharedCwithAB;
 253
 254                                         //find possible sharedABC values
 255                                         float sharedABC1 = 0.0; float sharedABC2 = 0.0; float sharedABC3 = 0.0; float sharedABC = 0.0;
 256
 257                                         if (vCalcs[i]->getMultiple() == false) {
 258                                                 //merge BC and estimate with shared with A
 259                                                 SharedRAbundVector* merge = new SharedRAbundVector();
 260                                                 for (int j = 0; j < lookup[1]->size(); j++) {
 261                                                         merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 262                                                 }
 263
 264                                                 subset.clear();
 265                                                 subset.push_back(lookup[0]); subset.push_back(merge);
 266                                                 sharedAwithBC = vCalcs[i]->getValues(subset);
 267
 268                                                 delete merge;
 269                                                 //merge AC and estimate with shared with B
 270                                                 merge = new SharedRAbundVector();
 271                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 272                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 273                                                 }
 274
 275                                                 subset.clear();
 276                                                 subset.push_back(merge); subset.push_back(lookup[1]);
 277                                                 sharedBwithAC = vCalcs[i]->getValues(subset);
 278
 279                                                 delete merge;
 280                                                 //merge AB and estimate with shared with C
 281                                                 merge = new SharedRAbundVector();
 282                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 283                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
 284                                                 }
 285
 286                                                 subset.clear();
 287                                                 subset.push_back(lookup[2]); subset.push_back(merge);
 288                                                 sharedCwithAB = vCalcs[i]->getValues(subset);
 289                                                 delete merge;
 290
 291                                                 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 292                                                 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 293                                                 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 294
 295                                                 //if any of the possible m's are - throw them out
 296                                                 if (sharedABC1 < 0.00001) { sharedABC1 = 0; }
 297                                                 if (sharedABC2 < 0.00001) { sharedABC2 = 0; }
 298                                                 if (sharedABC3 < 0.00001) { sharedABC3 = 0; }
 299
 300                                                 //sharedABC is the minimum of the 3 possibilities
 301                                                 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 302                                                 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 303                                                 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 304                                         }else{
 305                                                 vector<double> data = vCalcs[i]->getValues(lookup);
 306                                                 sharedABC = data[0];
 307                                                 sharedAwithBC.push_back(sharedAB[0] + sharedAC[0] - sharedABC);
 308                                                 sharedBwithAC.push_back(sharedAB[0] + sharedBC[0] - sharedABC);
 309                                                 sharedCwithAB.push_back(sharedAC[0] + sharedBC[0] - sharedABC);
 310                                         }
 311
 312                                         //image window
 313                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
 314                                         outsvg << "<g>\n";
 315
 316                                         //draw circles
 317                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 318                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.44 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 319                                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.33 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 320                                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.65 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 321                                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.5 * width)) +  "\" cy=\"" +  toString(int(0.5 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 322
 323                                         //place labels within overlaps
 324                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
 325                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 326                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 327                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
 328                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 329                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 330                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\"   y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
 331                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.52 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 332                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 333                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.34 * height)) +  "\">" + toString(sharedABC) + "</text>\n";
 334
 335                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
 336                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
 337                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
 338                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
 339                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.925 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
 340                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.95 * height)) +  "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
 341                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 342                                         if (numA.size() == 3) {
 343                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 344                                         }else { outsvg << "</text>\n"; }
 345
 346                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 347                                         if (numB.size() == 3) {
 348                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 349                                         }else { outsvg << "</text>\n"; }
 350
 351                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 352                                         if (numC.size() == 3) {
 353                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 354                                         }else { outsvg << "</text>\n"; }
 355
 356                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.80 * height)) +  "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
 357                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.975 * height)) +  "\">The total shared richness is " + toString(sharedABC) + "</text>\n";
 358
 359                                         delete singleCalc;
 360
 361                                 }else { //sharedchao and sharedsobs are multigroup
 362
 363                                         vector<SharedRAbundVector*> subset;
 364
 365                                         //get estimates for numA
 366                                         subset.push_back(lookup[0]);
 367                                         vector<double> numA = vCalcs[i]->getValues(subset);
 368
 369                                         //get estimates for numB
 370                                         subset.clear();
 371                                         subset.push_back(lookup[1]);
 372                                         vector<double> numB = vCalcs[i]->getValues(subset);
 373
 374                                         //get estimates for numC
 375                                         subset.clear();
 376                                         subset.push_back(lookup[2]);
 377                                         vector<double> numC = vCalcs[i]->getValues(subset);
 378
 379                                         subset.clear();
 380                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 381                                         vector<double> sharedab =  vCalcs[i]->getValues(subset);
 382
 383                                         subset.clear();
 384                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 385                                         vector<double> sharedac =  vCalcs[i]->getValues(subset);
 386
 387                                         subset.clear();
 388                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 389                                         vector<double> sharedbc =  vCalcs[i]->getValues(subset);
 390
 391                                         subset.clear();
 392                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 393                                         vector<double> sharedabc =  vCalcs[i]->getValues(subset);
 394
 395                                         //image window
 396                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
 397                                         outsvg << "<g>\n";
 398
 399                                         //draw circles
 400                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 401                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 402                                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.33 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 403                                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.65 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 404                                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.5 * width)) +  "\" cy=\"" +  toString(int(0.5 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 405
 406                                         //place labels within overlaps
 407                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
 408                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 409                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
 410                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 411                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 412                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
 413                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"   y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 414                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.51 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 415                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
 416                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.35 * height)) +  "\">" + toString(sharedabc[0]) + "</text>\n";
 417
 418                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
 419                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
 420                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
 421                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 422                                         if (numA.size() == 3) {
 423                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 424                                         }else { outsvg << "</text>\n"; }
 425
 426                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 427                                         if (numB.size() == 3) {
 428                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 429                                         }else { outsvg << "</text>\n"; }
 430
 431                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 432                                         if (numC.size() == 3) {
 433                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 434                                         }else { outsvg << "</text>\n"; }
 435
 436                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.8 * height)) +  "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
 437                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The total shared richness is " + toString(sharedabc[0]) + "</text>\n";
 438
 439
 440                                 }
 441
 442
 443                                 //close file
 444                                 outsvg << "</g>\n</svg>\n";
 445                                 outsvg.close();
 446
 447
 448                         }
 449
 450                 /******************* 4 Groups **************************/
 451
 452                 }else if (lookup.size() == 4) {
 453
 454                         height = 1600;
 455
 456                         //calc the shared otu
 457                         float sharedABCD = 0;
 458                         float numA = 0; float numB = 0; float numC = 0; float numD = 0;
 459                         float sharedAB = 0; float sharedAC = 0; float sharedBC = 0; float sharedAD = 0; float sharedBD = 0; float sharedCD = 0;
 460                         float sharedABC = 0; float sharedACD = 0; float sharedBCD = 0; float sharedABD = 0;
 461                         vector<double> data;
 462                         //get sabund vector pointers so you can use the single calculators
 463                         //one for each group
 464                         SAbundVector sA, sB, sC, sD;
 465                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC; SAbundVector* sabundD;
 466                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 467                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 468                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 469                         sD = lookup[3]->getSAbundVector();  sabundD = &sD;
 470
 471                         //A = red, B = green, C = blue, D = yellow
 472
 473                         //make a file for each calculator
 474                         for(int i=0;i<vCalcs.size();i++){
 475
 476                                 if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups.  It will be disregarded. "); m->mothurOutEndLine(); }
 477                                 else{
 478                                         string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 479                                         outputNames.push_back(filenamesvg);
 480                                         openOutputFile(filenamesvg, outsvg);
 481
 482                                         if (m->control_pressed) { outsvg.close(); return outputNames; }
 483
 484                                         //in essence you want to run it like a single
 485                                         if (vCalcs[i]->getName() == "sharedsobs") {
 486                                                 singleCalc = new Sobs();
 487                                         }else if (vCalcs[i]->getName() == "sharedchao") {
 488                                                 singleCalc = new Chao1();
 489                                         }
 490
 491                                         //get estimates for numA
 492                                         data = singleCalc->getValues(sabundA);
 493                                         numA = data[0];
 494         //cout << "num a = " << numA << endl;
 495
 496                                         //get estimates for numB
 497                                         data = singleCalc->getValues(sabundB);
 498                                         numB = data[0];
 499         //cout << "num b = " << numB << endl;
 500                                         //get estimates for numC
 501                                         data = singleCalc->getValues(sabundC);
 502                                         numC = data[0];
 503         //cout << "num c = " << numC << endl;
 504                                         //get estimates for numD
 505                                         data = singleCalc->getValues(sabundD);
 506                                         numD = data[0];
 507 //cout << "num d = " << numD << endl;
 508
 509                                         //get estimates for pairs
 510                                         subset.clear();
 511                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 512                                         data = vCalcs[i]->getValues(subset);
 513                                         sharedAB = data[0];
 514         //cout << "num ab = " << sharedAB << endl;
 515                                         subset.clear();
 516                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 517                                         data = vCalcs[i]->getValues(subset);
 518                                         sharedAC = data[0];
 519         //cout << "num ac = " << sharedAC << endl;
 520                                         subset.clear();
 521                                         subset.push_back(lookup[0]); subset.push_back(lookup[3]);
 522                                         data = vCalcs[i]->getValues(subset);
 523                                         sharedAD = data[0];
 524         //cout << "num ad = " << sharedAD << endl;
 525                                         subset.clear();
 526                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 527                                         data = vCalcs[i]->getValues(subset);
 528                                         sharedBC = data[0];
 529         //cout << "num bc = " << sharedBC << endl;
 530                                         subset.clear();
 531                                         subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 532                                         data = vCalcs[i]->getValues(subset);
 533                                         sharedBD = data[0];
 534                 //cout << "num bd = " << sharedBD << endl;
 535                                         subset.clear();
 536                                         subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 537                                         data = vCalcs[i]->getValues(subset);
 538                                         sharedCD = data[0];
 539
 540         //cout << "num cd = " << sharedCD << endl;
 541                                         //get estimates for combos of 3
 542                                         subset.clear();
 543                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 544                                         data = vCalcs[i]->getValues(subset);
 545                                         sharedABC = data[0];
 546                 //cout << "num abc = " << sharedABC << endl;
 547                                         subset.clear();
 548                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 549                                         data = vCalcs[i]->getValues(subset);
 550                                         sharedACD = data[0];
 551                         //cout << "num acd = " << sharedACD << endl;
 552                                         subset.clear();
 553                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 554                                         data = vCalcs[i]->getValues(subset);
 555                                         sharedBCD = data[0];
 556                 //cout << "num bcd = " << sharedBCD << endl;
 557                                         subset.clear();
 558                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 559                                         data = vCalcs[i]->getValues(subset);
 560                                         sharedABD = data[0];
 561 //cout << "num abd = " << sharedABD << endl;
 562                                         //get estimate for all four
 563                                         data = vCalcs[i]->getValues(lookup);
 564                                         sharedABCD = data[0];
 565                 //cout << "num abcd = " << sharedABCD << endl << endl;
 566
 567
 568
 569                                         //image window
 570                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
 571                                         outsvg << "<g>\n";
 572                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 573                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\" >Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 574
 575                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.625 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA) + "</text>\n";
 576                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.65 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB) + "</text>\n";
 577                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.675 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC) + "</text>\n";
 578                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.7 * height)) +  "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD) + "</text>\n";
 579
 580                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
 581                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
 582                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
 583                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.8 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
 584                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
 585                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</text>\n";
 586
 587                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
 588                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
 589                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.925 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
 590                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.95 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</text>\n";
 591
 592                                         //make adjustments
 593                                         sharedABC = sharedABC - sharedABCD;
 594                         //cout << "num abc = " << sharedABC << endl;
 595                                         sharedABD = sharedABD - sharedABCD;
 596                                 //cout << "num abd = " << sharedABD << endl;
 597                                         sharedACD = sharedACD - sharedABCD;
 598                                 //cout << "num acd = " << sharedACD << endl;
 599                                         sharedBCD = sharedBCD - sharedABCD;
 600                                 //cout << "num bcd = " << sharedBCD << endl;
 601
 602                                         sharedAB = sharedAB - sharedABC - sharedABCD - sharedABD;  //cout << "num ab = " << sharedAB << endl;
 603                                         sharedAC = sharedAC - sharedABC - sharedABCD - sharedACD;  //cout << "num ac = " << sharedAC << endl;
 604                                         sharedAD = sharedAD - sharedABD - sharedABCD - sharedACD;  //cout << "num ad = " << sharedAD << endl;
 605                                         sharedBC = sharedBC - sharedABC - sharedABCD - sharedBCD;  //cout << "num bc = " << sharedBC << endl;
 606                                         sharedBD = sharedBD - sharedABD - sharedABCD - sharedBCD; // cout << "num bd = " << sharedBD << endl;
 607                                         sharedCD = sharedCD - sharedACD - sharedABCD - sharedBCD;  //cout << "num cd = " << sharedCD << endl;
 608
 609                                         numA = numA - sharedAB - sharedAC - sharedAD - sharedABCD - sharedABC - sharedACD - sharedABD;
 610                         //cout << "num a = " << numA << endl;
 611                                         numB = numB - sharedAB - sharedBC - sharedBD - sharedABCD - sharedABC - sharedABD - sharedBCD;
 612                         //cout << "num b = " << numB << endl;
 613                                         numC = numC - sharedAC - sharedBC - sharedCD - sharedABCD - sharedABC - sharedACD - sharedBCD;
 614                         //cout << "num c = " << numC << endl;
 615                                         numD = numD - sharedAD - sharedBD - sharedCD - sharedABCD - sharedBCD - sharedACD - sharedABD;
 616                         //cout << "num d = " << numD << endl;
 617
 618                                         //draw circles
 619                                         outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 " +  toString(int(0.51 * width)) +  " " +  toString(int(0.27 * height)) +  ") \" cx=\"" +  toString(int(0.51 * width)) +  "\" cy=\"" +  toString(int(0.27 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 620                                         outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 " +  toString(int(0.51 * width)) +  " " +  toString(int(0.27 * height)) +  ") \" cx=\"" +  toString(int(0.51 * width)) +  "\" cy=\"" +  toString(int(0.27 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 621                                         outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 " +  toString(int(0.63 * width)) +  " " +  toString(int(0.36 * height)) +  ") \" cx=\"" +  toString(int(0.63 * width)) +  "\" cy=\"" +  toString(int(0.36 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 622                                         outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 " +  toString(int(0.36 * width)) +  " " +  toString(int(0.36 * height)) +  ") \" cx=\"" +  toString(int(0.36 * width)) +  "\" cy=\"" +  toString(int(0.36 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 623
 624                                         //A = red, B = green, C = blue, D = yellow
 625
 626                                         //place labels within overlaps
 627                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.66 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" +  toString(int(0.14 * height)) +  "\">" + toString(numA)  + "</text>\n";
 628                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.66 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.11 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 629                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"" +  toString(int(0.2 * height)) +  "\">" + toString(sharedAB) + "</text>\n";
 630                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.36 * width) - ((int)toString(numB).length() / 2)) + "\"  y=\"" +  toString(int(0.14 * height)) +  "\">" + toString(numB)  + "</text>\n";
 631                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.36 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.11 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 632                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"" +  toString(int(0.24 * height)) +  "\">" + toString(sharedAC) + "</text>\n";
 633                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.785 * width) - ((int)toString(numC).length() / 2)) + "\"   y=\"" +  toString(int(0.29 * height)) +  "\">" + toString(numC) + "</text>\n";
 634                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.785 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.26 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 635                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.31 * width) - ((int)toString(sharedBD).length() / 2)) + "\" y=\"" +  toString(int(0.24 * height)) +  "\">" + toString(sharedBD) + "</text>\n";
 636                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.22 * width) - ((int)toString(numD).length() / 2)) + "\"   y=\"" +  toString(int(0.29 * height)) +  "\">" + toString(numD) + "</text>\n";
 637                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.22 * width) - ((int)lookup[3]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.26 * height)) +  "\">" + lookup[3]->getGroup() + "</text>\n";
 638                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.34 * width) - ((int)toString(sharedAD).length() / 2)) + "\" y=\"" +  toString(int(0.41 * height)) +  "\">" + toString(sharedAD) + "</text>\n";
 639                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.675 * width) - ((int)toString(sharedBC).length() / 2)) + "\" y=\"" +  toString(int(0.41 * height)) +  "\">" + toString(sharedBC) + "</text>\n";
 640                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedCD).length() / 2)) + "\" y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(sharedCD) + "</text>\n";
 641                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.39 * width) - ((int)toString(sharedABD).length() / 2)) + "\" y=\"" +  toString(int(0.3 * height)) +  "\">" + toString(sharedABD) + "</text>\n";
 642                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.57 * width) - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"" +  toString(int(0.45 * height)) +  "\">" + toString(sharedBCD) + "</text>\n";
 643                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.435 * width) - ((int)toString(sharedACD).length() / 2)) + "\" y=\"" +  toString(int(0.45 * height)) +  "\">" + toString(sharedACD) + "</text>\n";
 644                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.63 * width) - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.3 * height)) +  "\">" + toString(sharedABC) + "</text>\n";
 645                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"" +  toString(int(0.4 * height)) +  "\">" + toString(sharedABCD) + "</text>\n";
 646
 647
 648
 649                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.975 * height)) +  "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD)) + "</text>\n";
 650
 651
 652                                         outsvg << "</g>\n</svg>\n";
 653                                         outsvg.close();
 654                                         delete singleCalc;
 655                                 }
 656                         }
 657                 }
 658
 659                 return outputNames;
 660
 661         }
 662         catch(exception& e) {
 663                 m->errorOut(e, "Venn", "getPic");
 664                 exit(1);
 665         }
 666 }
 667
 668